CHARMM c42b2 ssnmr.doc

File: SSNMR -=- Node: Top
Up: (commands.doc) -=- Next: Syntax

              Solid State NMR (SSNMR) Energy Functions


This module makes the SSNMR energy functions satisfying experimental data
observed in solid-state NMR. It focuses on 15N-chemical shifts and 15N-1H
dipolar couplings in a solid state. A set of these energy potentials are called
as orientational restraints providing us with the orientation information, such
as tilt, rotation, and etc. of in a particular helix. The module is specialized
on determining helix orientations in a bilayer. 

Please report problems to mack97hyuk@gmail.com or wonpil@ku.edu

References  : J. Lee, J. Chen, C. L. Brooks III, and W. Im,
              J. Magn. Reson. 193, 68-76(2008)
            : it includes the explanation of developement and application for 
              these restraints.

* Menu:

* 15N Chemical shift ::   Syntax of 15N chemical shift
* 15N Cheimical shift ::   Example of 15N chemical shift 
* 15N-1H dipolar coupling::   Syntax of 15N-1H dipolar coupling 
* 15N-1H dipolar coupling::   Example of 15N-1H dipolar coupling 

File: SSNMR -=- Node: 15N Chemical shift
Up: Top -=- Next: 15N Chemical shift -=- Previous: Top

1. 15N chemical shift

[SYNTAX]
CCS
EXPS [S11 real] [S22 real] [S33 real] [PHI real] 
ASSIGN atom-selection [FORCe real] [EXP real]
RESEt
PRINt ANALysis
END

S11, S22, S33:  Chemical shift tensors (ppm). They are obtained by diagonalizing
                a shielding tensor. These values are given from experiments.
                Refer Table1 in the above reference. 

PHI:            Phi angle (degrees) is defined by a rotation angle between NH
                vector and S11 chemical tensor on the peptide plane. It depends
                on the residues and also experimental conditions.

FORCe:          Force constant (unit: kcal/mol/ppm^2).
EXP:            Chemical shift observables from experiment (ppm).
atom-selection: Three atoms (NH, C, and O in peptide plane) consisting of
                chemical shift tensors.
RESEt:          Reset the assigned energy potentials
PRINt ANALysis: dump out junk data from the potentials

File: SSNMR -=- Node: 15N Chemical shift
Up: Top -=- Next: 15N-1H dipolar coupling -=- Previous: 15N Chemical shift

!----------CHARMM input--------------------------------------------------
! assign the experimental observables
set csexp8   76.50000
set csexp9   85.40000
set csexp10  72.60000

!set chemical shift force constant (kcal/mol/ppm^2)
set csforc 0.5 

!generate chemical shift potential
ccs
exps   s11 64.0 s22 77.0 s33 217.0 phi 107
assign sele ( resid  8 .and. ( type N .or. type HN )) .or. ( resid  7 .and. ( type C )) end -
       forc @csforc exp @csexp8
assign sele ( resid  9 .and. ( type N .or. type HN )) .or. ( resid  8 .and. ( type C )) end -
       forc @csforc exp @csexp9
assign sele ( resid 10 .and. ( type N .or. type HN )) .or. ( resid  9 .and. ( type C )) end -
       forc @csforc exp @csexp10
end

!dump out junk data from the assigned potentials
ccs
print anal
end

!get total energy
energy

!test first
test first sele ires 8:45 .and. (type N .or. type HN .or. type C) end

stop
!------------------------------------------------------------------------

File: SSNMR -=- Node: 15N-1H dipolar coupling
Up: Top -=- Next: 15N-1H dipolar coupling -=- Previous: 15N Chemical shift

2. 15N-1H dipolar coupling (any dipolar couplings are possible, such as 13C-1H
and etc.)

[Syntax]
CCS
EXPS [NUDC real] DCABs DIPC
ASSIGN atom-selection [FORCe real] [EXP real]
RESEt
PRINt ANALysis
END

NUDC:           Dipolar coupling constant; the value depends on the length of
                dipolar coupling vector (NH); in the case of NH vector length
                (1.07 Angstrom), it is ~19.86 kHz. If you want the simulation
                to be flexible dipolar coupling constant, use the keyword DCABs.
DCABs:          Flexible dipolar coupling constant will be used in the
                simulation.
DIPC:           It lets CHARMM to know the assingment to be dipolar coupling.
FORCe:          Force constant (unit: kcal/mol/kHz^2).
EXP:            Dipolar coupling observables from experiment (kHz).
atom-selection: Two atoms ( N/HN, CA/HA,and etc.) consisting of dipolar
                coupling.
RESEt:          Reset the assigned energy potentials
PRINt ANALysis: dump out junk data from the potentials

File: SSNMR -=- Node: 15N-1H dipolar coupling
Up: Top -=- Next: -=- Previous: 15N-1H dipolar coupling

!----------CHARMM input--------------------------------------------------
! assign the experimental observables
set dcexp7    -9.26125
set dcexp8   -11.09568
set dcexp9    -8.12626

!set dipolar coupling force constant (kcal/mol/kHz^2)
set dcforc 0.5 

!generate dipolar coupling potential
ccs
exps  nudc 19.86 ! DCABs
!DC
assign sele ( resid  7 .and. ( type N .or. type HN ))  end -
       DIPC forc @dcforc exp @dcexp7
assign sele ( resid  8 .and. ( type N .or. type HN ))  end -
       DIPC forc @dcforc exp @dcexp8
assign sele ( resid  9 .and. ( type N .or. type HN ))  end -
       DIPC forc @dcforc exp @dcexp9
end

!dump out junk data from the assigned potentials
ccs
print anal
end

!get total energy
energy

!test first
test first tol 0.000000001 sele ires 7:45 .and. ( type N .or. type HN ) end

stop
!------------------------------------------------------------------------